[2023-06-28 13:49:51,609] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:49:51,614] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:49:51,614] [INFO] DQC Reference Directory: /var/lib/cwl/stg04cf9d1b-8d95-421f-a667-6ce0d7df75e8/dqc_reference
[2023-06-28 13:49:52,801] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:49:52,802] [INFO] Task started: Prodigal
[2023-06-28 13:49:52,802] [INFO] Running command: gunzip -c /var/lib/cwl/stge622a5a0-1b57-4f0f-bafb-ee129382751e/GCA_017558665.1_ASM1755866v1_genomic.fna.gz | prodigal -d GCA_017558665.1_ASM1755866v1_genomic.fna/cds.fna -a GCA_017558665.1_ASM1755866v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:49:55,459] [INFO] Task succeeded: Prodigal
[2023-06-28 13:49:55,459] [INFO] Task started: HMMsearch
[2023-06-28 13:49:55,459] [INFO] Running command: hmmsearch --tblout GCA_017558665.1_ASM1755866v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04cf9d1b-8d95-421f-a667-6ce0d7df75e8/dqc_reference/reference_markers.hmm GCA_017558665.1_ASM1755866v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:49:55,610] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:49:55,611] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge622a5a0-1b57-4f0f-bafb-ee129382751e/GCA_017558665.1_ASM1755866v1_genomic.fna.gz]
[2023-06-28 13:49:55,629] [INFO] Query marker FASTA was written to GCA_017558665.1_ASM1755866v1_genomic.fna/markers.fasta
[2023-06-28 13:49:55,629] [INFO] Task started: Blastn
[2023-06-28 13:49:55,629] [INFO] Running command: blastn -query GCA_017558665.1_ASM1755866v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04cf9d1b-8d95-421f-a667-6ce0d7df75e8/dqc_reference/reference_markers.fasta -out GCA_017558665.1_ASM1755866v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:49:56,193] [INFO] Task succeeded: Blastn
[2023-06-28 13:49:56,196] [INFO] Selected 13 target genomes.
[2023-06-28 13:49:56,196] [INFO] Target genome list was writen to GCA_017558665.1_ASM1755866v1_genomic.fna/target_genomes.txt
[2023-06-28 13:49:56,197] [INFO] Task started: fastANI
[2023-06-28 13:49:56,197] [INFO] Running command: fastANI --query /var/lib/cwl/stge622a5a0-1b57-4f0f-bafb-ee129382751e/GCA_017558665.1_ASM1755866v1_genomic.fna.gz --refList GCA_017558665.1_ASM1755866v1_genomic.fna/target_genomes.txt --output GCA_017558665.1_ASM1755866v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 13:50:02,970] [INFO] Task succeeded: fastANI
[2023-06-28 13:50:02,970] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04cf9d1b-8d95-421f-a667-6ce0d7df75e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 13:50:02,971] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04cf9d1b-8d95-421f-a667-6ce0d7df75e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 13:50:02,981] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 13:50:02,981] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 13:50:02,981] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.7625	71	258	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	77.2069	60	258	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 13:50:02,982] [INFO] DFAST Taxonomy check result was written to GCA_017558665.1_ASM1755866v1_genomic.fna/tc_result.tsv
[2023-06-28 13:50:02,983] [INFO] ===== Taxonomy check completed =====
[2023-06-28 13:50:02,983] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:50:02,983] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04cf9d1b-8d95-421f-a667-6ce0d7df75e8/dqc_reference/checkm_data
[2023-06-28 13:50:02,984] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:50:03,000] [INFO] Task started: CheckM
[2023-06-28 13:50:03,000] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017558665.1_ASM1755866v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017558665.1_ASM1755866v1_genomic.fna/checkm_input GCA_017558665.1_ASM1755866v1_genomic.fna/checkm_result
[2023-06-28 13:50:17,224] [INFO] Task succeeded: CheckM
[2023-06-28 13:50:17,225] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 35.19%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 13:50:17,238] [INFO] ===== Completeness check finished =====
[2023-06-28 13:50:17,238] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:50:17,238] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017558665.1_ASM1755866v1_genomic.fna/markers.fasta)
[2023-06-28 13:50:17,239] [INFO] Task started: Blastn
[2023-06-28 13:50:17,239] [INFO] Running command: blastn -query GCA_017558665.1_ASM1755866v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04cf9d1b-8d95-421f-a667-6ce0d7df75e8/dqc_reference/reference_markers_gtdb.fasta -out GCA_017558665.1_ASM1755866v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:50:18,101] [INFO] Task succeeded: Blastn
[2023-06-28 13:50:18,105] [INFO] Selected 14 target genomes.
[2023-06-28 13:50:18,105] [INFO] Target genome list was writen to GCA_017558665.1_ASM1755866v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:50:18,114] [INFO] Task started: fastANI
[2023-06-28 13:50:18,114] [INFO] Running command: fastANI --query /var/lib/cwl/stge622a5a0-1b57-4f0f-bafb-ee129382751e/GCA_017558665.1_ASM1755866v1_genomic.fna.gz --refList GCA_017558665.1_ASM1755866v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017558665.1_ASM1755866v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:50:22,595] [INFO] Task succeeded: fastANI
[2023-06-28 13:50:22,602] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 13:50:22,602] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_017937195.1	s__CAG-83 sp017937195	85.879	214	258	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015067975.1	s__CAG-83 sp015067975	80.688	125	258	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015067525.1	s__CAG-83 sp015067525	80.6825	155	258	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017415775.1	s__CAG-83 sp017415775	80.1489	143	258	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015067765.1	s__CAG-83 sp015067765	78.354	70	258	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004555205.1	s__CAG-83 sp004555205	78.0226	90	258	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.21	98.12	0.89	0.88	3	-
GCF_018408575.1	s__CAG-83 sp000431575	77.7625	71	258	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.84	97.37	0.92	0.86	9	-
GCA_900555735.1	s__CAG-83 sp900555735	77.5492	75	258	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.84	99.67	0.89	0.81	3	-
GCA_002392625.1	s__CAG-83 sp002392625	77.4647	61	258	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.65	99.65	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-28 13:50:22,604] [INFO] GTDB search result was written to GCA_017558665.1_ASM1755866v1_genomic.fna/result_gtdb.tsv
[2023-06-28 13:50:22,604] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:50:22,606] [INFO] DFAST_QC result json was written to GCA_017558665.1_ASM1755866v1_genomic.fna/dqc_result.json
[2023-06-28 13:50:22,607] [INFO] DFAST_QC completed!
[2023-06-28 13:50:22,607] [INFO] Total running time: 0h0m31s